You only have to get rid of all shared state within the Micro constructor itself. For instance, with me.events = Micro.Pubsub; all instances will share the same Pubsub instance which is problematic, but you can solve that by instantiating a new Pubsub for every Micro instance. There is probably more shared state (e.g. document.querySelectorAll('[hub-link]')), but I haven't dug far.

Once you get rid of shared state within the Micro constructor, what would still be problematic though is to have multiple Micro instances using different sub-modules (e.g. Tpl, Routes). That is because you did not use any form of dependency inversion to resolve these sub-modules from within the Micro constructor.

That's probably not a problem though because I doubt a single application would ever use different sub-module implementations concurrently. Still, you may want to make dependencies explicit and allow to inject the sub-modules dependencies into the Micro constructor.